The Potters seal their passage into the latter stages of the competition after a late effort by the former Sunderland striker wiped out an unfortunate opener in the first half
Matthew Upson's own goal shortly before the half hour mark looked to have dented the hosts' qualification chances until the striker popped up with an equaliser in the closing 10 minutes to send Stoke through.
Potters boss Tony Pulis made eight changes from the side which defeated Blackburn at the weekend, handing rare starts to summer signings Upson, Wilson Palacios and Cameron Jerome.
As for the visitors, former AC Milan and Chelsea forward Andriy Shevchenko was given the opportunity to impress in front of an English audience after a disappointing spell at Stamford Bridge.
It was the Ukrainian side who started the brighter, twice coming close to opening the scoring through long-range efforts by Oleksandr Aliev. The first forced the recalled Asmir Begovic into a smart save, while the second attempt whistled just wide.
Dynamo Kiev finally got the reward their start deserved in the 27th minute though an Upson own goal as Shevchenko was allowed to run at the Stoke backline before laying off a pass to Aliev.
The impressive attacking midfielder's attempt took a wicked deflection off Upson’s outstretched boot and despite Begovic reaching the ball, the Bosnian stopper was unable to prevent it heading in.
Goalmouth scramble | Both sets of players challenge for the ball in the area
This home side’s supporters tried to get behind their team but the Potters failed to create anything before the break, and it was Shevchenko who came close to doubling his side’s lead only to fire against the outside of the post from a tight angle wide.
Stoke finally came to life in the second half and almost equalised early on through an unlikely source. Rory Delap played a delightful chipped ball past Kiev’s defence to anchorman Palacios, but the Ecuadorian could only fire straight at Oleksandr Shovkovskiy.
Shortly afterwards Jermaine Pennant drilled a fierce shot from just inside the penalty area which beat Shovkovskiy in Kiev’s goal, only to be cleared off the line by Yevhen Khacheridi.
Aware that an equaliser would clinch qualification to the knockout stage before their side’s final group game away to Besiktas, Stoke continued to press for a goal and finally got an equaliser in the 81st minute.
Former Arsenal man Pennant, whose final ball had been found lacking finally played in a superb bending cross which Jones did well to get his head to and power past Shovkovskiy.
Stoke knew a draw would be enough and managed to play out the final few minutes of the match thanks to a fine save in the final minute of the match by Begovic from a long distance Andriy Yarmolenko effort.
The result is enough to maintain the Potters' unbeaten record at home in European competition and seal their qualification into the latter stages of the competition.